Does this only happen with 'site rescan this' ? Have you applied the fix to 'site rescan' for the latest version of ioNiNJA?

Can you examine the filenames/pathnames and see if any of them have spaces or other weird characters like {[(' in them? I took a quick look at ioNiNJA and it does change permissions via [vfs write] in a few places and it just occurred to me that [vfs write <filename> 0 0 744] might somehow be ending up as 007 or something. I can't see why that would happen but it's the only thing I can think of...